I currently have an otu table that was generated from QIIME in the biom format. It comprises of 16S rRNA sequences that were annotated into OTUs. I used the biom convert command to create a tsv file, but the taxonomy names follow the Greengenes guidelines, where taxonomic levels are identified by k__(name); p__(name), and so forth to s__; , the species level.
Is there a flag within the biom commands which lets me parse the taxonomic levels as separate columns in the tsv file? I'm doing this so I can input the tsv table into R to analyze the data with vegan.